Could be (my guess) due to a memory issue in you machine due to your system
being very large or this could be a bug. Actually this happened to me
yesterday. Without using Amber 14, I tried Amber12 and Amber 11 (in a
different machine though) and the problem was gone in each of them. I know
this is not an ideal solution but that is what I have for now. This could
be a bug or a machine resource-dependent issue.
Sajeewa
On Tue, Apr 21, 2015 at 10:45 AM, Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Hi,
> thanks for pointing this out. Tail command on the inpcrd file says the
> following.
> Can you please suggest on how to fix this?
> Which parameters should I change in the leap.in file to give a sensible
> inpcrd file?
> Thanks.
> Vaibhav
>
> kmcdwlx005 462% tail P450_test.inpcrd
> 12.9410318 24.7763059 28.5292431 6.0666578 11.2373217 31.8421776
> 5.7263398 10.4381030 32.2442456 5.3605584 11.5374928 31.2698610
> 6.7183050 8.3222530 30.2949099 7.5409119 7.8483008 30.1727990
> 6.9621113 9.1013013 30.7947786 4.2421629 15.0141650 28.1041078
> 4.0966209 15.3281953 28.9965360 3.7646832 15.6326551 27.5511977
> 6.1018012 12.0044198 28.1521968 6.0879580 11.1085292 27.8154266
> 6.8190440 12.0114862 28.7860254 7.9544142 12.4381539 30.1975095
> 7.6961920 13.3598609 30.1959426 7.4229183 12.0411973 30.8875559
> 12.8990331 25.5432326 22.9765180 13.0727209 24.9778748 22.2239033
> 13.3919222 26.3433221 22.7944670 8.3746098 8.5713
> ukmcdwlx005 463%
>
> My current leap.in
> ukmcdwlx005 463% more leap.in
> source leaprc.ff14SB
> source leaprc.gaff
> CYP = loadmol2 CYS_HS.mol2
> set CYP head CYP.1.N
> set CYP tail CYP.1.C
> desc CYP
> HEM = loadmol2 HEM_pentacoordinateHS.mol2
> loadamberparams HEM_HS.frcmod
> loadamberparams frcmod.ionsjc_tip3p
> P450 = loadpdb 1W0E_P450_leap.pdb
> bond P450.419.SG P450.477.FE
> solvateoct P450 TIP3PBOX 12
> charge P450
> addions P450 Cl- 0
>
> On Tue, Apr 21, 2015 at 3:39 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>
> wrote:
>
> > Hi Vaibhav,
> >
> > What is the last line in your inpcrd file? Does it say something like
> > 90.0000 90.0000 90.0000 at the end? I bet it doesn't which means it
> doesn't
> > write the box dimensions and the angles to the inpcrd. So when sander
> > checks for them and cannot find them it gives the error message that you
> > reported.
> >
> > HTH
> >
> > Sajeewa
> >
> > On Tue, Apr 21, 2015 at 10:05 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >
> > wrote:
> >
> > > Ops, I meant the prmtop and inpcrd are ok in vmd, but the rst file was
> > not
> > > generated.
> > >
> > > On Tue, Apr 21, 2015 at 3:04 PM, Vaibhav Dixit <
> vaibhavadixit.gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > > I have checked with vmd, and it was OK.
> > > >
> > > >
> > > > On Tue, Apr 21, 2015 at 2:54 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > > > wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> Can you read the restart file with cpptraj or vmd or some other
> > program?
> > > >>
> > > >> -Dan
> > > >>
> > > >> On Tue, Apr 21, 2015 at 3:29 AM, Vaibhav Dixit <
> > vaibhavadixit.gmail.com
> > > >
> > > >> wrote:
> > > >> > Hi All,
> > > >> > while trying to run the minimization job on prmtop and inpcrd file
> > > >> > generated using ff14SB force field I am getting the this error
> > message
> > > >> in
> > > >> > the out file and sander quits quickly.
> > > >> > I have checked the unit before generating prmtop and inpcrd file
> and
> > > it
> > > >> > gave no error.
> > > >> > I am giving the following input to the sander.
> > > >> >
> > > >> > Another thread discussing similar error did not offer a clear
> > solution
> > > >> in
> > > >> > my case. http://archive.ambermd.org/201411/0298.html
> > > >> >
> > > >> > Any hints to trouble shoot this are much appreciated.
> > > >> > Thanks a lot.
> > > >> >
> > > >> > min.in
> > > >> > --------
> > > >> > P450 1W0E apo: initial minimization prior to
> > > >> > MD
> > > >> > &cntrl
> > > >> >
> > > >> >
> > > >> > imin=1,maxcyc=1000,ncyc=500,
> > > >> >
> > > >> >
> > > >> > ntpr=5,
> > > >> >
> > > >> >
> > > >> > cut=8.0,
> > > >> >
> > > >> >
> > > >> > ntc=2,
> > > >> >
> > > >> > ntr=1, restraintmask =
> > > >> > '.CA,C,O,N',
> > > >> >
> > > >> > restraint_wt=1.0
> > > >> >
> > > >> > /
> > > >> >
> > > >> >
> > > >> >
> > > >> >
> > > >> > --
> > > >> > With Regards.
> > > >> >
> > > >> > Dr. Vaibhav A. Dixit,
> > > >> > Postdoctoral Research Scientist,
> > > >> > Etherow F40/6,
> > > >> > AstraZeneca,
> > > >> > Charter Way,
> > > >> > Silk Road Business Park,
> > > >> > Macclesfield,
> > > >> > Cheshire,
> > > >> > England,
> > > >> > SK10 2NX
> > > >> > Ext. No. 20278
> > > >> > Email: Vaibhav.Dixit.astrazeneca.com
> > > >> > Moblie Number: +44-7448233157, +91-7709129400.
> > > >> >
> > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > > >> >
> > > >> > Please consider the environment before printing this e-mail
> > > >> > _______________________________________________
> > > >> > AMBER mailing list
> > > >> > AMBER.ambermd.org
> > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >>
> > > >>
> > > >> --
> > > >> -------------------------
> > > >> Daniel R. Roe, PhD
> > > >> Department of Medicinal Chemistry
> > > >> University of Utah
> > > >> 30 South 2000 East, Room 307
> > > >> Salt Lake City, UT 84112-5820
> > > >> http://home.chpc.utah.edu/~cheatham/
> > > >> (801) 587-9652
> > > >> (801) 585-6208 (Fax)
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > With Regards.
> > > >
> > > > Dr. Vaibhav A. Dixit,
> > > > Postdoctoral Research Scientist,
> > > > Etherow F40/6,
> > > > AstraZeneca,
> > > > Charter Way,
> > > > Silk Road Business Park,
> > > > Macclesfield,
> > > > Cheshire,
> > > > England,
> > > > SK10 2NX
> > > > Ext. No. 20278
> > > > Email: Vaibhav.Dixit.astrazeneca.com
> > > > Moblie Number: +44-7448233157, +91-7709129400.
> > > > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > > >
> > > > Please consider the environment before printing this e-mail
> > > >
> > >
> > >
> > >
> > > --
> > > With Regards.
> > >
> > > Dr. Vaibhav A. Dixit,
> > > Postdoctoral Research Scientist,
> > > Etherow F40/6,
> > > AstraZeneca,
> > > Charter Way,
> > > Silk Road Business Park,
> > > Macclesfield,
> > > Cheshire,
> > > England,
> > > SK10 2NX
> > > Ext. No. 20278
> > > Email: Vaibhav.Dixit.astrazeneca.com
> > > Moblie Number: +44-7448233157, +91-7709129400.
> > > http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
> > >
> > > Please consider the environment before printing this e-mail
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> With Regards.
>
> Dr. Vaibhav A. Dixit,
> Postdoctoral Research Scientist,
> Etherow F40/6,
> AstraZeneca,
> Charter Way,
> Silk Road Business Park,
> Macclesfield,
> Cheshire,
> England,
> SK10 2NX
> Ext. No. 20278
> Email: Vaibhav.Dixit.astrazeneca.com
> Moblie Number: +44-7448233157, +91-7709129400.
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> Please consider the environment before printing this e-mail
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 21 2015 - 08:00:03 PDT
